6-32038423-A-G

Variant names:

• chr6-32038423-A-G
• NM_000500.9:c.1A>G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000500.9(CYP21A2):​c.1A>G​(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CYP21A2 NM_000500.9 start_lost
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.17

Genes affected

CYP21A2 (HGNC:2600): (cytochrome P450 family 21 subfamily A member 2) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and hydroxylates steroids at the 21 position. Its activity is required for the synthesis of steroid hormones including cortisol and aldosterone. Mutations in this gene cause congenital adrenal hyperplasia. A related pseudogene is located near this gene; gene conversion events involving the functional gene and the pseudogene are thought to account for many cases of steroid 21-hydroxylase deficiency. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Start lost variant, next in-frame start position is after 10 pathogenic variants. Next in-frame start position is after 243 CDS bases. Genomic position: 32038762. Lost 0.163 part of the original CDS.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 6-32038423-A-G is Pathogenic according to our data. Variant chr6-32038423-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 1451630.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP21A2	NM_000500.9	c.1A>G	p.Met1?	start_lost	Exon 1 of 10	ENST00000644719.2	NP_000491.4
CYP21A2	NM_001128590.4	c.1A>G	p.Met1?	start_lost	Exon 1 of 9		NP_001122062.3
CYP21A2	NM_001368143.2	c.-424A>G		5_prime_UTR_variant	Exon 1 of 10		NP_001355072.1
CYP21A2	NM_001368144.2	c.-334A>G		5_prime_UTR_variant	Exon 1 of 9		NP_001355073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP21A2	ENST00000644719.2	c.1A>G	p.Met1?	start_lost	Exon 1 of 10		NM_000500.9	ENSP00000496625.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Oct 29, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects the initiator methionine of the CYP21A2 mRNA. The next in-frame methionine is located at codon 82. The frequency data for this variant in the population databases (gnomAD) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. Disruption of the initiator codon has been observed in individuals with classic salt-wasting, simple virilizing and non-classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency (PMID: 14676460, 23142378, 25227725, 31006099). It has also been observed to segregate with disease in related individuals. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.26
CADD	Benign	19
DANN	Benign	0.68
DEOGEN2	Benign	0.019	.;.;.;T;.;.
Eigen	Benign	-0.10
Eigen_PC	Benign	-0.073
FATHMM_MKL	Benign	0.49	N
LIST_S2	Uncertain	0.90	.;.;D;D;.;.
M_CAP	Pathogenic	0.85	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D
MetaSVM	Benign	-0.76	T
PROVEAN	Benign	-0.91	N;.;N;N;N;.
REVEL	Uncertain	0.41
Sift	Pathogenic	0.0	D;.;D;D;T;.
Sift4G	Uncertain	0.013	D;.;D;D;D;.
Polyphen		0.63	P;P;.;.;.;P
Vest4		0.86
MutPred		0.97		Loss of disorder (P = 0.0572);Loss of disorder (P = 0.0572);Loss of disorder (P = 0.0572);Loss of disorder (P = 0.0572);Loss of disorder (P = 0.0572);Loss of disorder (P = 0.0572);
MVP		0.95
ClinPred		0.71	D
GERP RS		4.5
gMVP		0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-32006200;